BioC 3.5: CHECK report for PathoStat on malbec2

Package: PathoStat

Version: 1.2.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PathoStat_1.2.1.tar.gz

StartedAt: 2017-10-18 01:22:18 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:27:02 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 283.9 seconds

RetCode: 0

Status:  OK

CheckDir: PathoStat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PathoStat_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/PathoStat.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathoStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathoStat’ version ‘1.2.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PathoStat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
runPathoStat    2.992  0.184   5.056
createPathoStat 2.064  0.060  19.401
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘PathoStat’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PathoStat)

name	user	system	elapsed
coreOTU	0.088	0.000	0.091
coreOTUModule	0	0	0
coreOTUModuleUI	0.608	0.000	0.621
coreOTUNormalize	0.056	0.000	0.054
coreOTUQuantile	0.024	0.000	0.021
createPathoStat	2.064	0.060	19.401
findRAfromCount	0.208	0.008	0.218
findTaxonLevel	0.088	0.000	0.768
findTaxonMat	0.352	0.000	2.960
findTaxonomy	0.264	0.000	2.714
getShinyInput	0	0	0
getShinyInputCombat	0.004	0.000	0.001
getShinyInputOrig	0.000	0.000	0.001
grepTid	0.004	0.000	0.001
loadPathoscopeReports	2.560	0.256	2.820
loadPstat	0.004	0.000	0.002
log2CPM	0.032	0.000	0.032
pathostat	0.316	0.000	0.331
plotConfRegion	0.764	0.016	0.780
readPathoscopeData	0.032	0.000	0.030
runPathoStat	2.992	0.184	5.056
savePstat	0.000	0.004	0.006
setShinyInput	0.000	0.000	0.001
setShinyInputCombat	0.000	0.000	0.001
setShinyInputOrig	0.000	0.000	0.001
sizeNormalize	0.024	0.000	0.025